imag is the imaginary (sine) part of the signal real is the real part (cosine) fsig is the significance (-log10(p)) where p is computed from an F test of the real and imag components
On 12/11/2014 05:09 AM, zhang mingxia wrote: > Thank you very much! > > The map opened by rtview seems correct. As a new learner of > retinotopic analysis, I have one more basic quesion: What do the three > files (imag.nii.gz, real.nii.gz and fsig.nii.gz) represent? Hope some > experienced one can reply me! > > Mingxia > > On Thu, Dec 11, 2014 at 12:14 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > On 12/08/2014 09:19 PM, zhang mingxia wrote: > > Hi Doug, > > > > I followed this guide: > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis. > > I used "tksurfer-sess" to view. Does "significant activation in the > > visual cortex" mean the map from"tksurfer-sess -a rtopy.self.?h -s > > sessid"? If so, yes. > > > > My question is (1) What do the maps from > > > "tksurfer-sess -a rtopy.self.?h -s sessid" -- this shows you the > > significance map (-log10(p)) with eccen and polar in different > frames > > in the tksurfer overaly. > > > , "tksurfer-sess -a rtopy.self.?h -s sessid -map angle" This > shows you > > the angle with eccen and polar in different frames in the > tksurfer overlay > > > , "tksurfer-sess -a rtopy.self.?h -s sessid -map angle.masked" This > > shows you the angle with eccen and polar in different frames in the > > tksurfer overlay with the angle masked to only those voxels that are > > significant (p<.01). > > > and "tksurfer-sess -a rtopy.self.?h -s sessid -fieldsign" represent? > > This shows you the field sign map. > > > > > (2)I expected to get a red, green and blue map, but none of them is. > > The first three are heat (yellow and red) and the fourth is > red-blue. > > This is the first time for me to do retinotopic analysis. The > data is > > from an experienced group for doing retinotopic research. I analyzed > > four runs with two for eccen and two for polar. Do other people also > > get this kind of color by using the script in the website above? > tksurfer-sess will not generate a RGB colorwheel map. This > functionality > has been hard to continue to support. You can try rtview. You > would use > the RGB map to show the angle maps. > > > > (3)Which map is for delineating the boarder of visual area? > field sign > > > > (4)Again, I expect to get a red, green and blue map as this people > > asked > > > > :https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21512.html. > > How can I get a standard color? > > > > Thanks again! > > > > Mingxia > > > > On Tue, Dec 9, 2014 at 12:07 AM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > > > I'm not sure what you are asking for. Do you see significant > > activation > > in the visual cortex? What command are you running to view? > > > > > > On 12/08/2014 09:48 AM, zhang mingxia wrote: > > > Dear freesurfer experts, > > > > > > I used Freesurfer 5 to do the retinotopic analysis followed by > > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis. > > > However, finally I didn't get a red, green and blue map as I > > expected. > > > > > > This is the first time for me to analyze retinotopic data. I > > have not > > > quite understood what the raw angle map, the angle map > masked by sig > > > and field sign map meant. My purpose was to delineate the > boarder of > > > visual area. To my knowledge from previous study, I should > get a > > > colorful map. It seems I didn't get a right one (However, > I exactly > > > follow the guide and didn't get any error). Some other > people seems > > > having the same viewing problem: (He/She didn't have eccen > data. I > > > have both eccen and polar data. I also only got a heat map > > instead of > > > a red, green and blue one) > > > > > > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21512.html > > > > > > (1)Is it due to the threshold? How can I get a red, green and > > blue map? > > > (2) What does the three maps represent? > > > > > > Thanks a lot! > > > > > > Mingxia > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the > person to > > whom it is > > addressed. If you believe this e-mail was sent to you in > error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
